5 papers
The Power of Graph Doubling: Computing Ultrabubbles in a Bidirected Graph by Reducing to Weak Superbubbles
Sebastian Schmidt, Juha Harviainen, Corentin Moumard +3
Bidirected graphs are a common generalisation of directed graphs where arcs can also be incoming to both their incident nodes, or outgoing from both their incident nodes. Such arcs…
Identifying bubble-like subgraphs in linear-time via a unified SPQR-tree framework
Francisco Sena, Aleksandr Politov, Corentin Moumard +6
A fundamental algorithmic problem in computational biology is to find all subgraphs of a given type (superbubbles, snarls, and ultrabubbles) in a directed or bidirected input graph…
Identifying all snarls and superbubbles in linear-time, via a unified SPQR-tree framework
Francisco Sena, Aleksandr Politov, Corentin Moumard +4
Snarls and superbubbles are fundamental pangenome decompositions capturing variant sites. These bubble-like structures underpin key tasks in computational pangenomics, including st…
Fast and Flexible Flow Decompositions in General Graphs via Dominators
Francisco Sena, Alexandru I. Tomescu
Multi-assembly methods rely at their core on a flow decomposition problem, namely, decomposing a weighted graph into weighted paths or walks. However, most results over the past de…
Safe Sequences via Dominators in DAGs for Path-Covering Problems
Francisco Sena, Romeo Rizzi, Alexandru I. Tomescu
A path-covering problem on a directed acyclic graph (DAG) requires finding a set of source-to-sink paths that cover all the nodes, all the arcs, or subsets thereof, and additionall…